Japanese Unexamined Patent Application Publication No. 2004-209626 (Patent Literature 1) has disclosed background art of the present technical field. The publication discloses the method of manufacturing the three-dimensional microstructure. The manufacturing method is implemented by producing a trial structure through temporary processing based on the designed three-dimensional configuration data of the three-dimensional structure while having processing conditions controlled so that the trial structure configuration is compared with the designed configuration. The main processing is performed while correcting the processing condition for the purpose of compensating for the difference.